Molecular Simulations of cotranslational protein folding: Fragment stabilities, folding cooperativity, and trapping in the ribosome
Molecular Simulations of cotranslational protein folding: Fragment stabilities, folding cooperativity, and trapping in the ribosome
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DOI：
10.1371/journal.pcbi.0020098
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发表时间：
2006-07-01
影响因子：
4.3
通讯作者：
Elcock, Adrian H.
中科院分区：
文献类型：
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作者：
Elcock, Adrian H.
尽管分子模拟方法对体外蛋白质重折叠的机制方面产生了有价值的见解，但迄今为止，它们尚未用于模拟蛋白质的折叠，因为它们实际上是由核糖体合成的。为了解决这个问题，我们在此报告了三种模型蛋白的模拟研究：胰凝乳蛋白酶抑制剂 2 (Cl2)、barnase 和 Semliki 森林病毒蛋白 (SFVP)，并直接比较它们在核糖体介导的合成过程中的折叠与它们从随机变性构象的重折叠。为了校准该方法，首先将模拟与 Cl2 和 barnase N 末端片段折叠稳定性的体外数据进行比较；模拟再现了这样一个事实：稳定性和热折叠协同性随着片段长度的增加而增加。然后描述了相同两种蛋白质的合成和折叠的耦合模拟，表明两种蛋白质基本上都是在翻译后折叠的，其机制与重折叠的机制实际上相同。在这两种情况下，将新生多肽链限制在核糖体通道内似乎并没有促进合成过程中天然结构的显着形成；然而，有明确的迹象表明，新生链内结构的形成对核糖体隧道内的位置敏感，随着链的延长，结构的形成会受到增益和损失的影响。有趣的是，人工稳定 Cl2 的模拟显示出一种明显的趋势，即以部分折叠构象被困在隧道内：因此，模拟中出现的非合作折叠对完全折叠构象的形成速率产生了不利影响。最后，对 SFVP 的双结构域蛋白酶模块（实验上以共翻译方式折叠）的模拟表明，对于多结构域蛋白质，核糖体介导的折叠可能遵循与重折叠过程中不同的途径。总而言之，这些研究为开发更现实的方法来模拟体内发生的蛋白质折叠提供了第一步。
Although molecular simulation methods have yielded valuable insights into mechanistic aspects of protein refolding in vitro, they have up to now not been used to model the folding of proteins as they are actually synthesized by the ribosome. To address this issue, we report here simulation studies of three model proteins: chymotrypsin inhibitor 2 (Cl2), barnase, and Semliki forest virus protein ( SFVP), and directly compare their folding during ribosome-mediated synthesis with their refolding from random, denatured conformations. To calibrate the methodology, simulations are first compared with in vitro data on the folding stabilities of N-terminal fragments of Cl2 and barnase; the simulations reproduce the fact that both the stability and thermal folding cooperativity increase as fragments increase in length. Coupled simulations of synthesis and folding for the same two proteins are then described, showing that both fold essentially post-translationally, with mechanisms effectively identical to those for refolding. In both cases, confinement of the nascent polypeptide chain within the ribosome tunnel does not appear to promote significant formation of native structure during synthesis; there are however clear indications that the formation of structure within the nascent chain is sensitive to location within the ribosome tunnel, being subject to both gain and loss as the chain lengthens. Interestingly, simulations in which Cl2 is artificially stabilized show a pronounced tendency to become trapped within the tunnel in partially folded conformations: non-cooperative folding, therefore, appears in the simulations to exert a detrimental effect on the rate at which fully folded conformations are formed. Finally, simulations of the two-domain protease module of SFVP, which experimentally folds cotranslationally, indicate that for multi-domain proteins, ribosome-mediated folding may follow different pathways from those taken during refolding. Taken together, these studies provide a first step toward developing more realistic methods for simulating protein folding as it occurs in vivo.